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mcmero / SVclone

A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.
BSD 3-Clause "New" or "Revised" License
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VCF input formats #11

Closed willhooper closed 4 years ago

willhooper commented 4 years ago

Hi,

I'm having some some trouble getting my VCFs to work with the filter step, and was wondering what the specific requirements were for each --snv_format option (sanger, mutect, mutect_callstats, consensus, multisnv). My raw mutect calls work fine with the mutect option, however I'd prefer to use my downstream calls that include additional callers and filters.

My apologies if this is already documented somewhere.

Thanks! Will

mcmero commented 4 years ago

Hi Will,

I've added some more information on the SNV VCF formats to https://github.com/mcmero/SVclone#snv-input-formats. Feel free to post any error messages you're getting from your filtered mutect calls if these options don't suit (a sample of the VCF file would be helpful as well).

Cheers, Marek

willhooper commented 4 years ago

Thanks Marek. After some tweaking of my VCFs I was able to get the mutect format working.